bmtk.utils package

Subpackages

• bmtk.utils.compile_mechanisms package
  • Submodules
  • bmtk.utils.compile_mechanisms.compile_mechanisms module
    • compile_mechanisms()
    • copy_modfiles()
  • Module contents
• bmtk.utils.create_environment package
  • Submodules
  • bmtk.utils.create_environment.create_environment module
    • create_environment()
  • bmtk.utils.create_environment.env_builder module
    • BioNetEnvBuilder
      • BioNetEnvBuilder.bmtk_simulator
      • BioNetEnvBuilder.compile_mechanisms()
      • BioNetEnvBuilder.examples_dir
      • BioNetEnvBuilder.target_simulator
    • EnvBuilder
      • EnvBuilder.base_dir
      • EnvBuilder.bmtk_simulator
      • EnvBuilder.build()
      • EnvBuilder.compile_mechanisms()
      • EnvBuilder.components_dir
      • EnvBuilder.examples_dir
      • EnvBuilder.network_dir
      • EnvBuilder.output_dir
      • EnvBuilder.scripts_root
      • EnvBuilder.target_simulator
    • FilterNetEnvBuilder
      • FilterNetEnvBuilder.bmtk_simulator
      • FilterNetEnvBuilder.examples_dir
      • FilterNetEnvBuilder.target_simulator
    • PointNetEnvBuilder
      • PointNetEnvBuilder.bmtk_simulator
      • PointNetEnvBuilder.examples_dir
      • PointNetEnvBuilder.target_simulator
    • PopNetEnvBuilder
      • PopNetEnvBuilder.bmtk_simulator
      • PopNetEnvBuilder.examples_dir
      • PopNetEnvBuilder.target_simulator
  • Module contents
• bmtk.utils.io package
  • Submodules
  • bmtk.utils.io.cell_vars module
    • CellVarRecorder
      • CellVarRecorder.DataTable
      • CellVarRecorder.add_cell()
      • CellVarRecorder.close()
      • CellVarRecorder.dt
      • CellVarRecorder.flush()
      • CellVarRecorder.initialize()
      • CellVarRecorder.is_initialized
      • CellVarRecorder.merge()
      • CellVarRecorder.record_cell()
      • CellVarRecorder.record_cell_block()
      • CellVarRecorder.tstart
      • CellVarRecorder.tstop
    • CellVarRecorderParallel
      • CellVarRecorderParallel.merge()
  • bmtk.utils.io.firing_rates module
    • RatesInput
      • RatesInput.get_rate()
      • RatesInput.populations
    • RatesWriter
      • RatesWriter.add_rates()
      • RatesWriter.to_csv()
      • RatesWriter.to_h5()
  • bmtk.utils.io.ioutils module
    • BMTKWorldComm
      • BMTKWorldComm.MPI_rank
      • BMTKWorldComm.MPI_size
      • BMTKWorldComm.barrier()
      • BMTKWorldComm.comm
    • set_world_comm()
  • bmtk.utils.io.spike_trains module
    • DFIndexedGIDs
      • DFIndexedGIDs.get_spikes()
    • DictIndexedGIDs
      • DictIndexedGIDs.get_spikes()
    • HDF5IndexedGIDs
    • PoissonSpikesGenerator
      • PoissonSpikesGenerator.to_hdf5()
    • SONATAIndexer
      • SONATAIndexer.get_spikes()
    • SpikeTrainWriter
      • SpikeTrainWriter.TmpFileMetadata
      • SpikeTrainWriter.add_spike()
      • SpikeTrainWriter.add_spikes()
      • SpikeTrainWriter.add_spikes_file()
      • SpikeTrainWriter.close()
      • SpikeTrainWriter.close_tmp_file()
      • SpikeTrainWriter.flush()
      • SpikeTrainWriter.to_csv()
      • SpikeTrainWriter.to_hdf5()
      • SpikeTrainWriter.to_nwb()
    • SpikesInput
      • SpikesInput.get_spikes()
      • SpikesInput.load()
    • SpikesInputCSV
      • SpikesInputCSV.get_spikes()
    • SpikesInputH5
      • SpikesInputH5.get_spikes()
      • SpikesInputH5.gids
      • SpikesInputH5.timestamps
    • SpikesInputNWBv1
      • SpikesInputNWBv1.get_spikes()
    • UnindexedGIDs
  • Module contents
    • log_warning()
• bmtk.utils.reports package
  • Subpackages
    • bmtk.utils.reports.compartment package
      • Submodules
      • bmtk.utils.reports.compartment.compartment_reader module
      • bmtk.utils.reports.compartment.compartment_report module
      • bmtk.utils.reports.compartment.compartment_writer module
      • bmtk.utils.reports.compartment.core module
      • bmtk.utils.reports.compartment.plotting module
      • Module contents
    • bmtk.utils.reports.spike_trains package
      • Submodules
      • bmtk.utils.reports.spike_trains.core module
      • bmtk.utils.reports.spike_trains.plotting module
      • bmtk.utils.reports.spike_trains.spike_train_buffer module
      • bmtk.utils.reports.spike_trains.spike_train_readers module
      • bmtk.utils.reports.spike_trains.spike_trains module
      • bmtk.utils.reports.spike_trains.spike_trains_api module
      • bmtk.utils.reports.spike_trains.spikes_file_writers module
      • bmtk.utils.reports.spike_trains.stats module
      • Module contents
  • Submodules
  • bmtk.utils.reports.current_writer module
    • CurrentWriterv01
      • CurrentWriterv01.DataTable
      • CurrentWriterv01.close()
      • CurrentWriterv01.dt()
      • CurrentWriterv01.flush()
      • CurrentWriterv01.initialize()
      • CurrentWriterv01.merge()
      • CurrentWriterv01.n_steps()
      • CurrentWriterv01.record_clamps()
      • CurrentWriterv01.set_dt()
      • CurrentWriterv01.set_tstart()
      • CurrentWriterv01.set_tstop()
      • CurrentWriterv01.set_units()
      • CurrentWriterv01.tstart()
      • CurrentWriterv01.tstop()
      • CurrentWriterv01.units()
  • Module contents
• bmtk.utils.sonata package
  • Subpackages
    • bmtk.utils.sonata.config package
      • Submodules
      • bmtk.utils.sonata.config.sonata_config module
      • Module contents
  • Submodules
  • bmtk.utils.sonata.column_property module
    • ColumnProperty
      • ColumnProperty.attributes
      • ColumnProperty.dimension
      • ColumnProperty.dtype
      • ColumnProperty.from_csv()
      • ColumnProperty.from_h5()
      • ColumnProperty.name
      • ColumnProperty.nrows
  • bmtk.utils.sonata.edge module
    • Edge
      • Edge.dynamics_params
      • Edge.edge_type_id
      • Edge.group_id
      • Edge.source_node_id
      • Edge.source_population
      • Edge.target_node_id
      • Edge.target_population
    • EdgeSet
      • EdgeSet.next()
  • bmtk.utils.sonata.file module
    • File
      • File.edges
      • File.has_edges
      • File.has_nodes
      • File.nodes
      • File.version
  • bmtk.utils.sonata.file_root module
    • EdgesRoot
      • EdgesRoot.edge_types_table
      • EdgesRoot.get_populations()
    • FileRoot
      • FileRoot.check_format()
      • FileRoot.get_population()
      • FileRoot.population_names
      • FileRoot.populations
      • FileRoot.root_name
      • FileRoot.types_table
    • NodesRoot
      • NodesRoot.generate_gids()
      • NodesRoot.has_gids
      • NodesRoot.node_types_table
      • NodesRoot.set_gid_table()
  • bmtk.utils.sonata.group module
    • EdgeGroup
      • EdgeGroup.build_indicies()
      • EdgeGroup.edge_type_ids
      • EdgeGroup.filter()
      • EdgeGroup.get_values()
      • EdgeGroup.next()
      • EdgeGroup.src_node_ids
      • EdgeGroup.to_dataframe()
      • EdgeGroup.trg_node_ids
    • Group
      • Group.all_columns
      • Group.build_indicies()
      • Group.check_format()
      • Group.column()
      • Group.columns
      • Group.get_dataset()
      • Group.get_values()
      • Group.group_columns
      • Group.group_id
      • Group.has_dynamics_params
      • Group.has_gids
      • Group.parent
      • Group.to_dataframe()
    • NodeGroup
      • NodeGroup.build_indicies()
      • NodeGroup.filter()
      • NodeGroup.get_values()
      • NodeGroup.gids
      • NodeGroup.node_ids
      • NodeGroup.node_type_ids
      • NodeGroup.to_dataframe()
  • bmtk.utils.sonata.node module
    • Node
      • Node.dynamics_params
      • Node.gid
      • Node.group_id
      • Node.group_props
      • Node.node_id
      • Node.node_type_id
      • Node.node_type_properties
      • Node.population_name
    • NodeSet
      • NodeSet.get_properties()
      • NodeSet.gids
      • NodeSet.next()
      • NodeSet.node_ids
      • NodeSet.node_type_ids
  • bmtk.utils.sonata.population module
    • EdgePopulation
      • EdgePopulation.build_indicies()
      • EdgePopulation.edge_types_table
      • EdgePopulation.filter()
      • EdgePopulation.get_row()
      • EdgePopulation.get_source()
      • EdgePopulation.get_source_population()
      • EdgePopulation.get_sources()
      • EdgePopulation.get_target()
      • EdgePopulation.get_target_population()
      • EdgePopulation.get_targets()
      • EdgePopulation.group_id_column
      • EdgePopulation.group_index_column
      • EdgePopulation.group_indicies()
      • EdgePopulation.next()
      • EdgePopulation.source_population
      • EdgePopulation.target_population
      • EdgePopulation.to_dataframe()
      • EdgePopulation.type_ids_column
    • NodePopulation
      • NodePopulation.add_gids()
      • NodePopulation.filter()
      • NodePopulation.get_gid()
      • NodePopulation.get_node_id()
      • NodePopulation.get_row()
      • NodePopulation.get_rows()
      • NodePopulation.gids
      • NodePopulation.group_id_column
      • NodePopulation.group_index_column
      • NodePopulation.has_gids
      • NodePopulation.igids()
      • NodePopulation.index_column_name
      • NodePopulation.inode_ids()
      • NodePopulation.inode_type_ids()
      • NodePopulation.next()
      • NodePopulation.node_ids
      • NodePopulation.node_types_table
      • NodePopulation.to_dataframe()
      • NodePopulation.type_ids_column
    • Population
      • Population.get_group()
      • Population.group_id_column
      • Population.group_id_ds
      • Population.group_ids
      • Population.group_index_column
      • Population.group_index_ds
      • Population.group_indicies()
      • Population.groups
      • Population.igroup_ids()
      • Population.igroup_indicies()
      • Population.name
      • Population.to_dataframe()
      • Population.type_ids
      • Population.type_ids_column
      • Population.types_table
  • bmtk.utils.sonata.types_table module
    • EdgeTypesTable
      • EdgeTypesTable.edge_type_ids
      • EdgeTypesTable.index_column_name
    • NodeTypesTable
      • NodeTypesTable.index_column_name
      • NodeTypesTable.node_type_ids
    • TypesTable
      • TypesTable.add_table()
      • TypesTable.column()
      • TypesTable.columns
      • TypesTable.find()
      • TypesTable.index_column_name
      • TypesTable.next()
      • TypesTable.to_dataframe()
      • TypesTable.type_ids
    • remove_nans()
  • bmtk.utils.sonata.utils module
    • add_hdf5_magic()
    • add_hdf5_version()
    • check_magic()
    • get_attribute_h5()
    • get_node_ids()
    • get_version()
    • listify()
    • load_csv()
    • load_h5()
  • Module contents

Submodules

bmtk.utils.hdf5_helper module

bmtk.utils.hdf5_helper.get_attribute_h5(h5obj, attribut_name, default=None)

bmtk.utils.sim_setup module

class bmtk.utils.sim_setup.BioNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)

Bases: EnvBuilder

property bmtk_simulator

compile_mechanisms()

property examples_dir

property target_simulator

class bmtk.utils.sim_setup.EnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)

Bases: object

property base_dir

property bmtk_simulator

build(include_examples=False, use_relative_paths=True, report_vars=[], report_nodes=None, clamp_reports=[], current_clamp=None, file_current_clamp=None, se_voltage_clamp=None, spikes_inputs=None, config_file='config.json', overwrite_config=False, **run_args)

property components_dir

property examples_dir

property network_dir

property node_sets_file

property output_dir

property scripts_root

property target_simulator

class bmtk.utils.sim_setup.FilterNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)

Bases: EnvBuilder

property bmtk_simulator

property examples_dir

property target_simulator

class bmtk.utils.sim_setup.PointNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)

Bases: EnvBuilder

property bmtk_simulator

property examples_dir

property target_simulator

class bmtk.utils.sim_setup.PopNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)

Bases: EnvBuilder

property bmtk_simulator

property examples_dir

property target_simulator

bmtk.utils.sim_setup.build_env_bionet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, overwrite_config=False, tstart=0.0, tstop=1000.0, dt=0.001, dL=20.0, spikes_threshold=-15.0, nsteps_block=5000, v_init=-80.0, celsius=34.0, report_vars=[], report_nodes=None, clamp_reports=[], current_clamp=None, file_current_clamp=None, se_voltage_clamp=None, spikes_inputs=None, compile_mechanisms=False, use_relative_paths=True, config_file=None)

bmtk.utils.sim_setup.build_env_filternet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, tstart=0.0, tstop=1000.0, config_file='config.json')

bmtk.utils.sim_setup.build_env_pointnet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, tstart=0.0, tstop=1000.0, dt=0.001, dL=20.0, spikes_threshold=-15.0, nsteps_block=5000, v_init=-80.0, celsius=34.0, report_vars=[], report_nodes=None, current_clamp=None, spikes_inputs=None, use_relative_paths=True, config_file=None)

bmtk.utils.sim_setup.build_env_popnet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, reports=None, include_examples=True, config_file=None, tstart=0.0, tstop=1000.0, dt=0.001, **args)

Module contents